Abstract

Alternative splicing (AS) shapes tumor biology by generating mRNA isoforms that regulate oncogenic signaling, immune modulation, and therapeutic response. However, its immune-related role in breast cancer (BRCA) remains insufficiently defined. Using TCGA-BRCA RNA-seq and clinical data, we quantified percent-spliced-in values with SpliceSeq and identified 1,063 differentially expressed AS events across 861 genes. These genes were enriched in cancer- and immune-related pathways, including focal adhesion, VEGF signaling, and cytokine-receptor interactions. Prognostic analyses revealed immune-associated AS events linked to overall survival and progression-free interval. Consensus clustering defined three AS-based subtypes with distinct immune landscapes and outcomes. C3 showed high immune infiltration, immune-activating molecule expression, and favorable prognosis, consistent with an immune-hot phenotype, whereas C1 displayed immunosuppressive features. Genomic alterations in splicing factors were associated with elevated tumor mutation burden, suggesting genomic instability may contribute to immune-related splicing dysregulation in BRCA.